To change the gender marker on your passport you must,
Submit the following documents (along with fees) in-person to any Passport Acceptance Facility:
A completed application for a U.S. Passport.
Proof of U.S. citizenship (ex: U.S. Passport, certified Birth Certificate, or a certificate of Naturalization)
Proof of identity with your signature (ex: State-issued License or ID)
A 2×2 color photograph of you
Legal name change order (only needed if changing name too)
A letter from a certified licensed physician or psychologist stating that you have transitioned or are in the process of transitioning
The fee to renew a passport or get a new passport.
*Note that f is not necessary if all other documents have the updated gender marker
** Also note if your doctor's letter states you are in the transition process, you will only receive a 2-year passport.
Find more information at the National Center for Transgender Equality.